1) They do not include the coupling coefficients.
2) The coupling coefficients give no useful information for the simulation engine after the signal has passed through the MMF, they are already coupled to the fiber modes after the fiber.
3) The coupling coefficients are calculated by performing an overlap integral of each input mode with each supported optical mode of the fiber. If you have the modes of the fiber and the input signal modes then yes you can calculate the coupling coefficients.
4)In the attached snapshot, I did a quick mockup. Using a fork you could make a copy of the input data and send it directly to the matlab component. Then inside your matlab component you could program the overlap integral and figure out how much power from each incident mode coupled into each fiber mode.
OR
If the mode shapes are not changing with your simulation just go to the MMF properties, the Report tab and click Generate report, this will give you a list of all the coupling coefficients which you could just copy into your .m file.